#!/bin/bash -e

function info() {
echo Usage: `basename $0` 'r1.fq r2.fq'
exit 2
}

while getopts  ":p:f:" opt; do
	case  $opt  in
		p) out_prefix=$OPTARG;;
		f) suffix=$OPTARG;;
		*) info;;
	esac
done
shift $(($OPTIND - 1))


if [ $# -lt 1 ]; then info; fi

. $var

echo;echo bsmap
bsmap -w 100 -v 5 -r 0 -s 16 -n 1 \
-p $threads \
-a $1 \
-d $ref_genome \
-o $out_prefix.1.sam

bsmap -w 100 -v 5 -r 0 -s 16 -n 1 \
-p $threads \
-a $2 \
-d $ref_genome \
-o $out_prefix.2.sam
# -m TC


. $cmd_done

